SingleCellAlleleExperiment
S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes
Bioconductor version: Release (3.20)
Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.
Author: Jonas Schuck [aut, cre] 
, Ahmad Al Ajami [aut] , Federico Marini [aut] , Katharina Imkeller [aut]
Maintainer: Jonas Schuck <jschuckdev at gmail.com>
citation("SingleCellAlleleExperiment")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SingleCellAlleleExperiment")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SingleCellAlleleExperiment")| An introduction to the SingleCellAlleleExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, Infrastructure, SingleCell, Software, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0), SingleCellExperiment |
| Imports | SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats |
| System Requirements | |
| URL | https://github.com/AGImkeller/SingleCellAlleleExperiment |
| Bug Reports | https://github.com/AGImkeller/SingleCellAlleleExperiment/issues |
See More
| Suggests | scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | scaeData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleCellAlleleExperiment_1.2.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | SingleCellAlleleExperiment_1.2.0.tgz |
| macOS Binary (arm64) | SingleCellAlleleExperiment_1.1.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SingleCellAlleleExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SingleCellAlleleExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/SingleCellAlleleExperiment/ |
| Package Short Url | https://bioconductor.org/packages/SingleCellAlleleExperiment/ |
| Package Downloads Report | Download Stats |